Harvard University officially confirmed Monday that it had secretly gained access to the ­e-mail accounts of 16 resident deans and apologized for the discomfort it caused, but said that doing so was necessary to safeguard the privacy of students caught up in last year’s cheating scandal.

The university’s statement — released by Michael Smith, the dean of the Faculty of Arts and Sciences, and Evelynn Hammonds, dean of the college — did not fully quell the controversy on campus and drew an emphatic response from a key figure in the case.

Senior resident dean Sharon Howell disputed a portion of the statement that said administrators had told her about the search shortly after it took place.

Howell maintained that she had not been officially ­informed until last week, after the Globe approached Harvard asking about the search, which was sparked by the leak of a confidential ­e-mail about last year’s cheating scandal.

On Monday afternoon, Howell sent an impassioned letter to Harvard president Drew Faust on behalf of many of the resident deans, asking Faust to directly address the matter and begin a “new conversation about integrity at Harvard.”

Late Monday afternoon, Faust said in a statement that she felt “very comfortable that great care was taken to safeguard the privacy of all concerned” in the incident, but that she shared “the view that questions about whether more resident deans should have been informed sooner are fair to ask.”

“I believe that debates about the rights and responsibilities of members of our community are healthy,” she said.

Faust’s statement further said that she had been ­informed in September of a ­potential breach in confidentiality surrounding the school disciplinary board’s handling of the cheating case and was also told the concern had been ­resolved, but was not ­“informed of specifics.”

Smith and Hammonds’s statement officially confirmed for the first time that a limited search had occurred after admin­istrators decided that the leak might have “threatened the privacy and due process ­afforded students before the board.” That search concluded that one of the deans had forwarded a confidential e-mail to two students she was advising, after which it essentially went viral and landed in the hands of The Harvard Crimson, the student newspaper.

The statement further said that although the content of the leaked e-mail itself could be viewed as “not particularly consequential,” administrators had been alarmed by its appearance in the media in the context of another incident in which “confidential data from an Administrative Board meeting was shared with the Crimson.”

The leak of that information, reported in the Crimson on Sept. 11, was not investigated.

The statement from Smith and Hammonds further said that prior to the e-mail account search, Howell in her capacity as the senior resident dean “was asked to reach out individually” to the other resident deans to see if someone would come forward as the leaker, but that her request had “yielded no insights.”

Howell said that she did ask the other deans if they knew how the leaked e-mail, meant to be confidential, had made its way to the media. But she ­emphasized that at the time she was approaching the other resident deans, no administrator had raised the possibility of searching e-mail accounts, much less said definitively that a search would occur.

The Smith and Hammonds statement also said that Howell “was immediately informed of the search, and its outcome” shortly after the fact, a point Howell disputed vigorously. She reiterated her earlier statement to the Globe that administrators did not tell her, “verbally or otherwise,” that the search had happened until last week. She did learn of it before then, she added, but only because the dean who forwarded the e-mail had confided in her.

Another Harvard official, who asked to remain anonymous, said he had met with Hammonds several months ago and been told that only the dean in question would be advised of the search; the others, including Howell, would not.

In response Monday afternoon, Smith and Hammonds appeared to stand by their statement that Howell had been informed, as well. A university official who asked to ­remain unnamed told the Globe that “both the dean of the college and the secretary of the Administrative Board recall sharing the outcome of the search with the senior resident dean. They also requested that she reach out and lend support to the resident dean who had been implicated, which she did and which we appreciated now and then.”

The original statement from Smith and Hammonds contained an apology “if any resident deans feel our communication at the conclusion of the investigation was insufficient.”

It was unclear how that apology was being received. Howell and others who had spoken with the resident deans said the group was feeling vulnerable and that the university’s house masters — professors who, like the resident deans, live with students — were angry on their behalf.

Meanwhile, the episode was provoking considerable ­debate, especially among faculty. Several professors said they thought the issue would be raised at an Administrative Board meeting on Tuesday and a Faculty Council meeting on Wednesday.

Harry Lewis — the former dean of the college, current computer science professor, and frequent thorn in the admin­istration’s side — wrote on his blog that he would “probably, after four decades, respond by moving most of my personal and frivolous e-mail” to a Google mail account.

Lewis also raised a concern about the privacy of other ­Harvard e-mail account holders, including the thousands of graduates who maintain alumni addresses. “Given the university’s encompassing view of its rights to scan ‘employee’ e-mail, including faculty e-mail when the faculty have administrative responsibilities,” he wrote, “I would not assume that the university would feel constrained.”

On another blog, two other Harvard computer science professors — Michael Mitzenmacher and Greg Morrisett — wrote that they felt the episode had been “blown out of proportion.”

But both emphasized the need for faculty members and administrators to further hash out the issues involved.

Morrisett, who had initially expressed serious concern about the incident, elaborated in an e-mail to the Globe. “For the most part, I think that [Smith] and the rest of the admin­istration actually did the right things,” he wrote. “The one failing is that they didn’t ­inform the other resident deans that they were doing the search, and there’s enough of a ‘mea culpa’ in his statement to mollify me regarding this particular incident.”

However, Morrisett said, he would like administrators to clarify whose e-mail privacy was protected under the Faculty of Arts and Sciences policy and to “affirm the policy and promise to abide by it in the ­future.”

He suggested that the dean consult “a small, select group of faculty when he is ­going to do such a search . . . to create more trust about the situation.”

Sandra Korn, a junior who participates in many activist groups, said the episode had ­reminded her of a worry she had heard in years past but dismissed as unrealistic.

While organizing the 2011 Occupy Harvard protest, she said, she had been told by graduate students not to write about the group’s plans on her Harvard e-mail account. “I think the undergraduates were skeptical that the administration would be poking through our e-mails,” she said. “I still doubt that anyone was doing that. But I guess it was good we were cautious.”

Another student, who was implicated and later exonerated in the cheating case, said he felt that in gaining access to the resident deans’ accounts, admin­istrators might have compromised the student privacy they were seeking to protect, because students use those accounts to communicate confidentially with their resident deans about disciplinary issues.

As for the cheating scandal as a whole, he added, with an air of exasperation, “I didn’t think it could get any more ­ridiculous.”